


Starts and stops

by TiffanyF



Series: Closing the Rift [1]
Category: Torchwood
Genre: AU, M/M, ooc
Language: English
Status: Completed
Published: 2013-01-13
Updated: 2013-05-14
Packaged: 2017-11-25 07:11:26
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 11
Words: 13,364
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/636408
Author URL: https://archiveofourown.org/users/TiffanyF/pseuds/TiffanyF
Summary: <blockquote class="userstuff">
              <p>A AU piece on how Ianto came to work at Torchwood 3 with Jack. Please note I have yet to watch Torchwood (it's next on my list) so this is based off of youtube videos. Don't own, don't claim, no money made here.</p><p>Jack will die at least once, I just wasn't sure if that should be a warning or not.....</p>
            </blockquote>





	1. Chapter 1

"You can't go!" Lisa insisted as Ianto slipped on his jacket. "Ianto, it's Torchwood. You saw what happened in London at Canary Wharf. Why would you even want to try and go back to them?"

"Because this Torchwood is different," Ianto replied. "This is where I should have been all along. This is where I belong."

"Ianto Jones, don't you dare walk out that door," Lisa shouted as he shut the door to their apartment behind him. They'd met at Torchwood London, fallen in love, moved in together and then Canary Wharf happened. He wasn't sure what Lisa saw when hiding from the Cybermen and the Daleks, or even how she managed to hide from them, but it changed her. A part of Ianto knew he was only staying out of guilt. Lisa could barely stand to be in the same room with him, they'd had separate bedrooms since she'd come home from the hospital, and she only yelled at him, never talked like they used to. He wanted, needed, to move forward, understand exactly what he'd seen at Canary Wharf, find someone who really knew about aliens and could help him work the events into his worldview.

All his research and contacts pointed to the same man; Captain Jack Harkness of Torchwood Three in Cardiff. Ianto was cautioned that the Captain would flirt with anything on two legs, possibly even aliens themselves, and that was the only reason Ianto chose to wear his tightest jeans, fitted shirt and short jacket. He was hoping he'd be able to catch the Captain's eye and manage to get a job with Torchwood 3.

Of course, the rest of the night didn't go anywhere close to what Ianto had planned, he got a nasty cut on his head, but he learned that Captain Jack Harkness looked good in the long WWII era coat he always wore. Ianto spent the rest of the night trying to convince himself the reason his body felt like it was on fire was because he hadn't slept with anyone in over six months.  
**********

Meeting with the Captain in the morning with a mug of his specially made coffee was risky, Ianto knew, but he wanted to officially ask for a position. He was a little surprised at how quickly Jack turned him down, but Ianto felt a strange heat flood through him when Jack he'd checked Ianto out. The other man had a logical and reasonable reason behind his research, yet Ianto wondered if there might be something else to it, something not even the Captain was willing to admit to.

Ianto felt Jack's eyes sweep his face, taking in the bruises and swollen lip that hadn't been there the night before, and weren't a result of the weevil attack, but Jack didn't say anything about it. As Jack left, Ianto made it a point to call after him how much he really liked Jack's coat.  
**********

For their third meeting, Ianto left the club image at home and dressed in one of his older suits, knowing that any type of fieldwork with Torchwood could get messy very quickly. He left Lisa sleeping and snuck out into the night. It wasn't hard to work out where Jack was heading, and Ianto really was quite fond of the dinosaur that fell through the rift.

The lack of supplies worried him a little though. "That's your specialist equipment?" he asked.

"Yeah, because I keep dinosaur nets in the SUV," Jack replied.

That was the moment when Ianto realized Captain Jack Harkness lived for one thing, and that was adventure. The problem was that it really was hard not to get caught up in his enthusiasm.

"It's quite excitable," Jack said, leaning back against the metal door.

"Must be your aftershave," Ianto said. He had been fighting a growing urge to bury his face against Jack's neck and just breathe for a while.

"I never wear any," Jack replied.

"You smell like that naturally?" Ianto asked, shocked. No human should be able to smell that good without some sort of chemical aid.

"Fifty-first century phermones," Jack said, sounding almost smug, "you people have no idea."

Ianto had no clue how to reply to that, so he let it go and followed Jack back into the warehouse to try and capture the dinosaur. Ending up catching Jack after the Captain sedated the flying dinosaur, while he was hanging onto it's leg, wasn't exactly what Ianto expected, but he had to roll them so they wouldn't be crushed and didn't have time to think about it. Not before he realized Jack was under him and their mouths were almost touching. Ianto gazed down into Jack's eyes and realized it was a moment of choice. He could walk away and go back to the mess his life turned into after Canary Wharf, or he could kiss the man under him and see what happened next.

Would it be cheating on Lisa if he kissed Jack? Ianto wasn't even sure what their relationship was at that point. It had been months since he'd been able to touch her, forget about anything more. The only time she touched him was when she hit him, and that was becoming an almost daily event.

When put that way, it wasn't much of a choice. Ianto closed the distance between them and caught Jack's mouth with his own. Jack's hands tightened on his shoulders as he gave himself over, almost as if he was able to sense what Ianto was thinking.

"How long will that trank work?" Ianto whispered against Jack's lips.

"Not long enough for what I'd love to do to you," Jack replied. He reached up and touched Ianto's face softly. "Unless you need to get home, that is."

"She doesn't know I'm gone," Ianto said. "I don't even know if I should go home or not."

Jack pressed a soft kiss to the corner of Ianto's mouth, almost directly over the cut. "Come with me and at least have a drink," he said. "We can talk, no strings attached."

"What about her?" Ianto asked, nodding towards the dinosaur.

"We'll take her with us. I really do have a place for her," Jack said. "There's a place for you too, if you want it."

Ianto knew he should get up, that it wasn't proper to by lying on top of another man, but the contact felt too good to lose. "What sort of place?" he asked.

"Office manager and refreshment for now," Jack said. "Full access to the archives if you want to organize them, research the aliens who were at Canary Wharf, and find out about the universe. Maybe even more, if you want it."

"I've never done this before," Ianto said.

"Then it's a good thing you have me as a teacher, isn't it?" Jack grinned. He kissed Ianto again. "Come on, let's get the beauty over there taken care of and we'll talk."  
**********

"You live under your office?" Ianto asked, staring at the hole in the floor. He almost couldn't believe Jack was serious.

"The rift needs to be monitored constantly and I don't trust machines to do it right," Jack replied. "We can talk up here if you'd be more comfortable."

"No, it's fine, I was just surprised." Ianto shifted around and climbed down the ladder into Jack's bedroom, as it turned out.

"Sorry about the mess," Jack said, dropping next to Ianto. "I wasn't expecting company. Make yourself at home."

Ianto slipped off his suit jacket and draped it neatly over the back of the only chair in the room before sitting down. "Tell me the truth, did you hire me this time because I kissed you?"

"Nope." Jack handed him a tumbler with some sort of whiskey in it and sat down on the edge of his bed. "I hired you because you don't give up, won't back down, are smart, think fast on your feet and aren't afraid to speak up. I need someone like that around here."

"From the looks of things, you really do need a butler," Ianto commented dryly. 

"I told you, it's been a busy week," Jack said. "So, do you want to tell me about it?"

Ianto looked down at his glass. "You said you checked me out."

"In more ways than one," Jack grinned. "You mean I saw you have a girlfriend?"

"Lisa. She managed, somehow, to hide at Canary Wharf and wasn't found until the rescue workers got there," Ianto said. "I spent the attack locked in a vault deep in the basement. I don't know anyone even knew it was there, just the researcher I was working with, and he killed himself rather than let the aliens get him. I don't even know how long I was in there for, but there were supplies. Lisa was in the hospital when I finally came out of hiding."

"She ever talk about what happened to her?"

"No, but it changed her for the worse," Ianto said. "She won't let me near her, she has nightmares, and she won't talk unless it's to yell at me for some reason."

Jack sighed. "How long has she been hitting you?" he asked softly.

"Since I started researching you and Torchwood 3," Ianto replied. "I decided that I want to learn about aliens, help protect the Earth from the bad ones so no one else has to suffer through what I did. Lisa doesn't want me near Torchwood, so she's been growing violent. I just don't know if it's to push me away, or something she's not telling me about."

"You said the bad ones just now," Jack said. "Does that mean you think there are good aliens out there?"

"There has to be, does't there?" Ianto asked. "Just like there are good people and bad people, I think there must be good aliens to counter the bad. Otherwise, what's the point to the universe?"

Jack grinned. "Oh, there are some very good aliens out there, some of the nicest beings you'll ever meet," he said. "They have no interest in the Earth, though, so they'll never come here. There's just one who does, and no one else ever believes me about him."

"You've met aliens?"

"I suppose, technically, I am one, even if I'm human," Jack said. "I'm from the fifty-first century, Ianto. I came here because I knew I would be able to find the one person I'm looking for here, someday. My Doctor will be here, one day."

"Well, that explains some of your comments today," Ianto said. "So what happens now?"

"Now it's all up to you. What do you want, Ianto Jones? What do you want for yourself?"

"This would be so much easier if we were still high on the thrill of the chase," Ianto said, looking at Jack.

"Easier for you to make an excuse to yourself in the morning, or easier to forget you're sleeping with a man for the first time in your life?" Jack asked.

"I don't think I'd be able to ignore the fact that you're a man," Ianto said. "I just can't work out if wanting to sleep with you means I'm cheating on Lisa."

"Do you want to wait until you talk with her?"

Ianto shook his head. "She wouldn't really hear what I was saying," he said. "I'm more concerned about what she might do when she learns I've got a new job with Torchwood."

"That's an easy enough problem to fix," Jack said, "if you want to move out, I'll come with you. She's far less likely to be violent if there's a stranger around."

"Where would I go?"

"You can use the flat I keep as a cover until you find a place of your own," Jack said. "I almost never stay there, so you wouldn't be putting me out."

"Do you do this for all your new employees?"

"Just the ones who look good in suits," Jack grinned. "Shall we go?"

"Yeah, might as well get it over with."


	2. Chapter 2

Ianto unlocked the door to the flat he shared with Lisa quietly, hoping that she might still be asleep and he would be able to grab his clothes without their usual morning confrontation.

He wasn't that lucky.

Ianto's heart sank when he caught sight of Lisa sitting on the sofa, arms crossed, staring at the door. "Morning," he said, moving to the side to let Jack into the room.

"Where the hell have you been?" Lisa demanded. "Who is that?"

"Captain Jack Harkness, ma'am," Jack replied with one of his more charming smiles. "You must be Lisa. It's a pleasure to meet you."

"Who is he, Ianto?" Lisa asked.

"My new boss," Ianto replied. "The Captain is head of Torchwood 3 and decided that I'm a good match for their team. I start first thing tomorrow morning."

"I told you I didn't want you near Torchwood again, Ianto," Lisa snapped, standing up.

"Lisa, one of us needs to be working. Our savings are almost gone, we need money coming in," Ianto said. "I know you think that your family will help us, and maybe they would, but I'm not going to sit around and do nothing. Not when I'm able to work and know what's really out there. I'm still young and able to do something about it. I need to do this. I need to be able to understand. I had hoped you would be happy for me."

"Happy?" she spat. "How could I possibly be happy that you're going back to work for a group that nearly got the whole Earth killed?"

"Never happen, the Doctor wouldn't let it," Jack said. He really wanted a closer look at the apartment, but he wasn't going to leave Ianto's side. Something wasn't sitting right with him, and Jack learned many years past to trust his instincts. "My guess is that someone at Torchwood London managed to stall the Doctor just long enough, and that's the only reason things went as bad as they did."

"Like you know anything about it," Lisa said.

"I know more than you think I know," Jack said softly. "My team and I were around doing what we could to help without direct confrontation with the Cybermen or the Daleks. We saved a fair number of innocents before the Doctor worked his magic and saved the world. Just like he always does."

Ianto couldn't help but notice the longing in Jack's voice and made a note to ask him about it later. "Lisa, I'm going back to Torchwood. The Captain has cut all ties with London and it's not the group we worked for. It's better. They are actually working to save people, actively protecting them, not the research crap we did in London."

"What about my parents? They're expecting us to come stay starting this weekend," Lisa said. "I've closed out the lease here, our things are going to my parents' house. They're really looking forward to it."

"Lisa," Ianto sighed, "I'm sure they are, but I'm not going to be going. Our relationship has changed so much in the last six months that I'm not even sure where I stand anymore. It's almost like you want a boyfriend without the romance and affection that naturally comes with it. I think the best thing for us both is for you to go to your parents and find a new balance in life for yourself. Find someone you can trust enough to talk with about what happened to you at Canary Wharf."

"You're leaving me?" she demanded.

"I'm doing what is best for us both, no matter how much it hurts," Ianto said. "I've been here, Lisa, every day for more than six months and I can't do it anymore. It's like we're living in a bubble and you won't even realize that I'm here with you. All you seem to want from me is a punching bag, and I won't be that for you. It's not fair to either of us. I can't do that anymore."

Jack, who hadn't taken his eyes off Lisa since her focus shifted to Ianto, caught the move first. He pushed Ianto out of the way just as the gun that appeared in Lisa's hand discharged. "Damn it," he muttered when he felt the bullet tear into his chest.

"Lisa, what did you do?" Ianto cried. He knelt next to Jack and felt almost frantically for a pulse. "He's dead."

"It was supposed to be you," Lisa said, eyes fixed on the blood pooled on the floor. "It should be you."

"Lisa, you don't want to do this," Ianto said. He wondered, absently, if he should be worried his biggest concern was for Jack's coat. He couldn't help but remember the mysterious way Jack's wounds seemed to heal. "I don't know what happened to you in London, but this isn't you. The woman I fell in love with didn't have an ounce of violence in her soul. Don't let what happened change that. There's enough violence in the world without us adding to it like this. Put the gun down and let's talk."

"No, there's nothing left to talk about," Lisa said. "There's nothing left to do but die."

"That's not true, Lisa, there's always something left to talk about. What about your parents? How do you think they're going to feel when they find out about all of this?" Ianto asked. "Lisa, you still have people who love you. My leaving doesn't mean I don't still love you. It just means that we've come to a point where we need to be apart for a while. We both need the time and space to think about what we want from life. It's not time to die. We're both still young and there's a reason we both survived Canary Wharf. How can we say we're just going to throw all that away?"

Ianto wanted to be focused on Jack, on the man who turned every single thing he believed about himself on its head, but he knew that if he took his eyes off Lisa for a second, she would shoot him. He had to pin all his hopes on a hope she wouldn't shoot him while he was looking into her eyes. Ianto wasn't sure what he was hoping Jack would do, the man was dead on the floor, but he was from the future and he wasn't from Earth. There had to be something more that he hadn't told Ianto.

"You don't know what you're talking about," Lisa said. "You never have. You don't understand, Ianto, and you won't. Not until you die. You have to die to understand."

"No one else has to die today, Lisa. Put the gun down and we'll go to your parents' house," Ianto said. "You know your mom will have your room all ready for you, and the guestroom ready for me. We can tell her you're not feeling well and she'll make your favorite soup to help settle your stomach. Won't that be nice? You haven't seen your mum in months, I know you've missed here, being here in Cardiff. Come on, just put the gun down and we'll go see your mum."

The bright blue light that shot from the floor and wrapped around Lisa was so sudden that Ianto fell over backwards in shock. Jack caught Lisa as she fell towards the floor and put her down gently. "That hurt," he commented.

"Jack?"

"She's just stunned, won't wake up for hours," Jack continued. "Let me take her back to the Hub and have our doctor look her over. Some of the things she was saying were a little too close to the Cybermen for comfort."

"Jack?"

"What, Ianto?"

"You're alive," Ianto said. He crawled over and reached out, finger sliding into the bullet hole in Jack's shirt. "You were dead. You died. Lisa shot you and you died."

"I'm fine," Jack said with a soft smile. He stood and took off his coat. "The cleaner just got this back to me. He's going to be livid I got blood on it again this soon."

Ianto stood up and reached out to touch Jack's chest, feeling the strong heartbeat under his fingers. "Is it bad that I want to throw you down on the floor and ravish you?" he asked softly.

"The timing would be awkward," Jack replied just as softly. He pulled Ianto in against him, holding the shaking man tightly. "Let me get my team here to take care of everything and we'll have another talk. I promise we'll get to the ravishing, but I want us both clean and rational. At least at the beginning."

"I suppose I have to move my stuff too, don't I?" Ianto asked. "What am I going to tell her parents?"

"Will you trust me to take care of everything?" Jack asked in reply.

"Yes," Ianto whispered.

Jack leaned in and kissed Ianto softly. Ianto felt all the tension flow out of his body. He wasn't sure how, but Jack was alive. For once, in as long as he could remember, Ianto could lean on someone else and let them worry about everything. Ianto realized all he wanted to do was sleep.


	3. Chapter 3

Ianto wound up back in Jack's bedroom and in his bed. Alone. Jack had stayed long enough to show Ianto where everything was, loan him something to sleep in, and tuck him into bed. He'd promised not to tell anyone Ianto was there, that no one ever dared venture into his personal space and Ianto would be safe.

He lay there and slowly managed to relax. Ianto knew he should be up and with Lisa, supporting and reassuring her that everything was going to be fine. That they would find a way to fix it all and Lisa would be fine again. He should be the good boyfriend, the strong one who chased away all her fears and kept her calm while she was surrounded by strangers, but Ianto just couldn't do it. He was exhausted. He'd been so focused on Lisa since she was released from the hospital that he'd ignored his own needs, and he was too exhausted to stand. He wanted to sleep, needed to sleep, but every time he closed his eyes, Ianto saw Jack's fall to the ground and the look on Lisa's face, almost blocked by the gun, but still obvious. 

He jumped when the hatch overhead opened, and sat up, letting the blankets pool in his lap. "Jack?"

"You're supposed to be asleep," Jack said, hopping off the ladder.

"I can't," Ianto admitted. "Every time I try, I see you dying or Lisa trying to kill me. How is she?"

"Owen has her sedated and is running some tests to see what's going on with her," Jack said. "He'll let me know if he finds anything. Now how about you? How are you holding up?"

"It all seems like some sort of a dream," Ianto sighed. "All of it, from the invasion in London to Lisa shooting you. How can you still be alive?"

"It's complicated, Ianto, and I don't fully understand it, but something was done to me before I came to Earth. Something that brings me back any time I die," Jack said. He sat down in the chair and rubbed his face. "One day, maybe I'll find the one being in this universe who can explain it to me, but until then, I'm just really glad I'm the way I am."

Ianto slipped out of the bed and into Jack's lap, feeling foolish, but wanting to be closer to the other man. "Do you mind?"

"Not at all," Jack smiled. He wrapped his arms around Ianto's back and pulled him in closer, helping to stabilize him. "You know, for having never been with a man before, you sure seem comfortable with all of this."

"I don't know why," Ianto admitted softly. "I've never felt like this around another man before. I've never wanted to kiss another bloke, or share a bed with one." He lifted his head just enough that he could meet Jack's eyes. "Why now? Why with you?"

"I don't have an answer for that, Ianto," Jack said. "I could see your struggle at the warehouse, but figured that was just because you have a girlfriend and you didn't want to cheat on her. I didn't know that you'd never kissed a man before. You did it with such ease that, if we hadn't had Myfanwy to deal with, you probably would have lost your virginity there on the floor."

Ianto turned a deep red and hid his face against Jack's neck. He hadn't felt so embarassed since Lisa had come back to the apartment and caught him looking at a sex toy web page. That night had led to a spectacular row between them and a sleepless night for Ianto. Jack seemed to catch his mood and started to rub his back softly. "Sorry, I shouldn't tease," he said. "That's who I am, Ianto. I'm a pretty blunt guy with a shady past. Are you sure you want to risk yourself with me?"

"I'm sure," Ianto said. He paused. "There's someone listening in up there."

"Owen, is that you?" Jack called.

"Yeah, sorry, didn't know you had company over," Owen replied. "I've got the initial readings back if you two want to come take a look at them."

"Ianto?"

He shook his head. "I'll stay here. I don't want to see her hooked up to machines again. I don't think I can do it."

"All right then. Rest, even if you don't sleep. There are some books in that box there by the bathroom door if you want to read," Jack said. He kissed the top of Ianto's head and stood with the other man in his arms. "We need to feed you, you're way too light."

"Jack."

"Rest. I'll be back when I can." Jack kissed his forehead and started up the ladder. He closed the hatch behind him and turned to Owen. "You know better than to eavesdrop on me, Owen, so why don't you tell me what the hell you thought you were doing?"

"I'm just curious about our new tea-boy is all," Owen said. "It's not like you to hide employees away like this, Jack. You normally bring them right into the thick of everything and expect them to work no matter what."

"He just watched his girlfriend try to kill someone, Owen. Plus he was in the thick of Canary Wharf. I think he's earned a chance to sleep, don't you?" Jack asked, almost pushing the doctor out the door.

"Yeah, sure, just saying it's not like you is all," Owen said. He led the way towards the autopsy theater. "The initial blood work on Lisa came back as normal. She's been starving herself, might want to ask why that is, or maybe her boyfriend has been starving her. You never know with some people."

"Owen, I'm only going to say this once, so I want you to make damn sure you're listening to me," Jack snapped. "Ianto is as much of a victim here as Lisa is. He's been doing everything in his power to help her since Canary Wharf and she repaid him by trying to kill him. Lay off."

"Fine, fine," Owen said. "Took a few scans of her brain, knowing there were Cybermen at Canary Wharf, but subtle isn't exactly their forte, is it? Didn't find anything that looks out of place, but Tosh is looking at them to make sure I didn't miss some teeny-tiny bit of tech, but I don't think I did."

Jack sighed and looked at the sedated woman. "Put her in the cells for now. Make sure she's taken care of," he said. "I have an idea for someone who might be able to give us a little more help. I just need to find out how to contact him."


	4. Chapter 4

Jack hadn't seen or heard from the Doctor since he was abandoned on the Game Station. He knew that the Time Lord would be the best one to help him, probably the only one in the universe who really knew about the daleks and the Cybermen, but would he come and help? Jack didn't even know if there was a way to get a hold of him, let alone if the Time Lord would come. He sent his team home and went back to his office to think. With a small sigh, he opened up his vortex manipulator and started at it. No more time travel with it, but it could still do so much. He supposed it was possible that he could use it to send a message out in hopes that it would find the Doctor.

"What are you doing?"

"You're quiet," Jack commented. He turned in his chair and held out his arms. "Come here before you freeze, Ianto."

"Where is everyone?" Ianto settled against Jack with a soft sigh. Having someone around who was stronger than him was not a bad thing at all.

"I sent them home. Lisa's secure, for now, and I know someone who might be able to help. I just need to get a hold of him," Jack replied. "You're still not asleep, Ianto."

"I don't know if I'll ever be able to sleep again," Ianto admitted.

Jack kissed his forehead. "Okay, you can stay here and watch me puzzle this out," he said. 

"Why can't you just use the phone?"

"Tell me what you know about the Doctor, Ianto. What did Torchwood London tell you about him?"

"The Doctor? He's the reason Torchwood was created by the royal family," Ianto said. "One of the main enemies of the crown, we're to capture and secure him on sight."

"Yeah, that's about what I thought you'd say. I've met him, Ianto. The Doctor." Jack smiled softly. "He really is as mad as Torchwood London seemed to think he was, but it's a good sort of mad. He will never walk away if there's someone who needs him, will always be able to solve the problem in the end."

"Do you love him, Jack?" Ianto asked softly.

"How can I not? He saved me, Ianto, saved me from myself and then he left me again," Jack replied. "I know that I should hate him for that, but the years have tempered the anger. He abandoned me, left me on a dead station surrounded by the dead, but I know there has to be a reason he did it. I've been searching for him all these years, but haven't found him in the right timeline yet."

Ianto leaned back a little. "Right timeline?"

"There's so much I could teach you, Ianto Jones," Jack said. "So much that is out there, in the universe, just waiting to be found by humans."

"So, teach me," Ianto said.

"Maybe I will, but first we have to get Lisa sorted," Jack sighed. He shifted the man in his lap a little until he could reach his vortex manipulator. "I think this is the best way to get in touch with him, but what do I say? I can't bring him into Torchwood, Suzie would shoot him on sight. Owen and Tosh would want to study him, it just wouldn't work."

"What if we could sneak him in?" Ianto asked. "Have him come when the team is gone and get him out again before they come back?"

Jack snorted. "His driving leaves a lot to be desired, there's no way to know when he would get here." He looked at his wrist and sighed. "Oh well, I'll just have to keep him safe. Can't keep Lisa secure forever, she needs to be able to live."

"Trying to get rid of me, Jack?" Ianto asked softly.

"Nope, trying to get rid of her so I can have you all to myself," Jack said. He nudged Ianto's head with his nose and caught the other man's lips when they appeared. "You have no idea how much I'm holding back right now."

"What if I don't want you to hold back?"

"Your first time is going to be magical, Ianto Jones," Jack said. He stood up, Ianto in his arms, and headed towards the bunker. "You need to eat, you're too light."

"I'm not hungry," Ianto admitted. "I haven't been in a long time."

"You will be. We'll start you off with something light and see what we can tempt you with. Now, come on, you need your sleep so you can start working tomorrow. I think I'm in withdrawl from your coffee."

"You only had one sip," Ianto pointed out.

Jack set him down and closed his vortex manipulator. "That wasn't enough for me," he said. "Go on down, I'm just going to check a few things and I'll join you. We're starting anew tomorrow, Ianto, and it could be a very long day."


	5. Chapter 5

Ianto, somehow, managed to fall asleep once Jack was in the bed holding him. He would have sworn he was only asleep for a minute when he heard something that woke him up. "Jack?"

"Yeah, I'm awake," Jack replied. "Get dressed, Ianto. That's our helper."

"I thought you weren't going to contact him until tomorrow." Ianto rubbed his eyes and slipped out of the small bed, looking for the pair of jeans he'd brought with him.

"I didn't. Or, rather, he must have got the message before I sent it." Jack put on a dress shirt like a jacket and started up the ladder. "Come on up when you're dressed."

Jack had a lot of practice on the ladder and was up in his office quickly, not wanting to chance the Doctor running away again. His eyes landed on a young man in a tweed jacket with. "A bow-tie?" he asked.

"It's cool. Bow-ties are cool," the young man said. "Hello Jack Harkness."

"Doctor?"

"Yes." The Doctor wrung his hands. "I really shouldn't be the one who is here, Jack, but I've skipped a few timelines to help you out. The me you knew died almost immediately after the Game Station, and it's not time for you to meet the Doctor who comes next in your timeline. I couldn't just leave you to deal with this on your own though, not when I got your message. It was too important, and what's important to you is important to me. Hello, this must be Ianto Jones. How very nice to meet you, Ianto Jones. Jack told me a lot about you."

"Doctor."

"Yes, quite. Sorry, Jack. Rambling. It's only seemed to get worse. Still, many things improved, and that's the most important bit," the Doctor said. "Now, tell me about Lisa. What's been going on?"

Jack perched on his desk and motioned for Ianto to join him. "Doctor, how far in my future are you?" he asked. "How do you know about Ianto and Lisa?"

"Oh, Jack, I'm sorry, but I can't tell you. I wish I could, but I've already endangered a couple of timelines by coming here," the Doctor said. "The less you know about me now, the better off you'll be the next time you see me. Well, see the previous me. Well, see the me that your Doctor turned into."

"I get it," Jack said, trying not to laugh. He wasn't too sure about meeting the Doctor in the right timeline, but he already felt fond for the one standing in front of him. "Regeneration isn't what I thought it was."

"Of course it's not, no one understand it," the Doctor said. "Now then, Ianto Jones. The man who survived Canary Wharf. Tell me what you think happened to Lisa."

Ianto didn't know what to think. Torchwood, the Torchwood he knew, had always talked about the Doctor like he was some sort of a monster, someone who would endanger the Earth. The man standing in front of him looked like someone who wouldn't be out of place at a university. He was wearing a bow-tie. "I don't know," he finally said, stepping between Jack's legs and leaning back for support. "She's changed so much, but even with how violent she's become, I never thought she'd shoot anyone."

"Yes, well, Jack's special," the Doctor smiled. "I'm glad he is, the universe would be a darker place without you, Jack Harkness." He clapped his hands. "Now, I know you want to keep me away from your team, so, show me where Lisa is and let me see if I can figure out what's gone wrong."

"Do you want to stay here, Ianto?" Jack asked softly.

"No, I'm going to come along," Ianto replied. "I'll stay back so I'm not in the way, but I owe it to Lisa to be with her."

"Good man," the Doctor said. "Lead the way, Jack."

Jack sighed. He itched to ask the Doctor all the questions that had been nagging at him since the Game Station, but couldn't. Messing with timelines was dangerous and Jack wouldn't do anything to risk ones that the Doctor was already playing with. The Time Lord understood time better than any being in the universe, and Jack wasn't about to try and second guess him. Not when there was so much in the balance. "This way," he said. He waited until Ianto was clear to hop down and start out into the Hub and towards the cells. "Where's the beautiful girl, Doctor?"

"Close by, but well hidden," the Doctor replied. "I wasn't sure how your team, how Torchwood would react to seeing her, so I made sure that she would be safe."

"There's not many of us here," Jack admitted. "Just five, with Ianto joining us. Five humans against the rift. I don't like those odds, Doctor, but what else can I do?"

"Nothing," the Doctor said. "You're doing everything you can, unless you want me to find a way to close the rift for good."

"You could do that?" Jack asked.

"Probably, maybe, with time," the Doctor replied. "I would have to study it, and that would mean being here while your team was around. I know you don't want me to meet them, Jack."

"I just don't know how they would take to you," Jack admitted. "She's in here."

The Doctor pulled out what had to be his sonic screwdriver, even if it didn't look anything like Jack remembered it. "Sonic screwdriver, Doc?" he asked with a smile.

"Yes, Jack, and I still say it's better than your sonic blaster," the Doctor said. He scanned Lisa and flicked his wrist, studying the readings. "Jack, you know about the daleks and the cybermen. What's the one thing they have in common?"

"Other than hating the human race, uhm, they remove emotions from their victims," Jack said. He reached over and put an arm around Ianto's shoulder, pulling him in close. "The cybermen remove all emotions, the daleks can leave hate, but even that is rare."

"It is, yes. The daleks I've been seeing lately have been poorer copies than those that died in the Time War," the Doctor said. "Can I go in there with her?"

"Will you be safe?" Jack asked.

"You tell me, how asleep is she?"

"I dunno. I told Owen to make sure she was taken care of, but I don't know how long the drugs he used to sedate her will last," Jack said.

"Well then, why don't you come in with me?" the Doctor asked. "You've always been a much better fighter than I am, and you're certainly stronger than me this time."

Jack laughed. "Don't even, Doctor. I fell for that once, so not going to do it again," he said.

"Jack?" Ianto asked.

"The Doctor is a Time Lord, Ianto. An alien, one who is stronger than humans, even by my time. He could pick me up with one hand right now and not even break a sweat," Jack replied.

"Just so you know, I prefer for people not to know that about me," the Doctor said.

"Speaking of people, I should've asked sooner. Where's your current companion?" Jack asked. 

"They're visiting friends," the Doctor said. "I'm going to meet them in the morning. Well, if I can't go in with her, I suppose I can just use one of these holes to try and get a better reading then."

"Can you tell what's wrong with her, Doctor?" Ianto asked.

"Not without running some more detailed tests, I'm afraid," the Doctor sighed. He looked at the sonic again. "Jack, I'm going to need to take her to the TARDIS and run some tests there. Will you help me restrain her, just in case she wakes up while we're moving?"

"Yeah, no problem, but we're coming along," Jack said.

"I'd be shocked if you didn't want to," the Doctor sighed. "Jack, you have to stay out of the TARDIS. You can wait outside, I won't leave, but the timelines...."

"Fine," Jack said. "How big of a paradox would we cause if I stepped into the TARDIS again, tonight?"

"I don't know, but given that I've already had the universe blow up several times, I'd rather not find out," the Doctor said.

Ianto looked puzzled. "The universe blew up?" he asked. "How are we all still here then?"

"I fixed it," the Doctor said, only just managing not to look offended by such a question.


	6. Chapter 6

Ianto closed his eyes while Jack and the Doctor secured Lisa and brought her out of the cell. His feelings for her were more confused than ever, but he didn't want to see her hurt. She'd meant so much to him for so long that he was starting to wonder if he'd done the right thing.

"Come on," Jack said softly, holding Lisa in his arms. "We're going to take her as far as the door and then the Doctor will take over and we can either get some sleep or get something to eat."

"She looks so peaceful," Ianto said. "I haven't seen her sleep in months. Doctor, do you really think you can help her?"

"Yes, although I'm not sure exactly what's wrong with her," the Doctor replied. "I might have to get some help, Ianto Jones, and that could take a while. Will you trust me to do all of this?"

"Would it cause a paradox if I went with you?" Ianto asked.

"Yes." The Doctor looked at Jack. "Teach him about timelines, Jack. Get something to eat and start teaching him. One day I'll come back and take you both on a grand adventure, but now is not the time." He stopped in front of an empty area well back in the hub. "I'll take it from here, Captain."

Jack looked around. "Where is she, Doctor?"

"I've learned a few tricks since you saw me last, Jack." The Doctor snapped his fingers and suddenly there was an opening in front of him. Ianto stared into it, amazed. The Doctor smiled. "Yes, she is beautiful, isn't she?"

"She's invisible?" Jack laughed. "How long has she been able to do that? That would have saved us all a few headaches a time or two."

"It's an old trick, one I don't use much anymore," the Doctor said. He took Lisa and stepped inside the TARDIS. "It's so easy to forget where you parked."

Jack started laughing as the door closed behind the Doctor. Ianto even managed a smile. "I can see why you like him so much, Jack."

"You have no idea," Jack said. "Come on, there's still some pizza in the kitchen and you can make friends with the coffee machine. None of us can work it, it just grumbles at us and won't do anything. I'm hoping you'll have better luck because that coffee of yours is magical, Ianto."

"Jack, is it safe to leave them alone?"

"As safe as can be. The Doctor won't hurt anyone," Jack said. He took Ianto's hand and pulled him towards the kitchen. "Not without fair warning, at least one chance to run away and they have to really, really deserve it. There's so much about him that even I don't know, because my Doctor never really talked about himself, but I do know that Lisa is safer with him than she would be on her own here."

"Thank you," Ianto said softly. He tugged on Jack's hand and kissed him when the other man looked back. "I'm still not sure what my feelings for her are, but I don't want her hurt. Not when she's obviously hurting so badly already. Now then, where's this coffee machine of yours?"  
*******  
The Doctor took Lisa through to the medical bay and secured her to a table. "Subtle isn't how the Cybermen or the Daleks operate, Lisa, but I think that we'll be safer with you secure," he said. "Sexy, will you make sure these are strong enough to hold back a Cyberman, please? I don't want to risk Lisa getting lose in here. It's possible this was all set up as a trap for me, and Jack didn't realize that."

"Doctor?"

"Rory, I thought you went with Amy to visit friends," the Doctor said, not turning around.

"Yeah, well, she wanted girl time with them and I wasn't going to argue," Rory replied. He joined the Time Lord in the medical bay. "Who's this?"

"This is Lisa, and I'm not sure what's happened to her," the Doctor said. "Actually, it's a good thing you're here, Rory. Will you take her vitals and let me know if they're normal for a human of her age, please?"

"Sure," Rory said. He wasn't too sure what was going on, but had learned not to question the Doctor. He dug out his things and went over to the young woman on the table. "Are these restraints really necessary?"

"Yes, Rory, I'm afraid they are," the Doctor sighed. "Until I'm sure she's not a danger to herself, or to us, she needs to stay restrained. That means no telling Pond about her if I'm still trying to work this out when we pick her up."

"Okay," Rory nodded. He fell silent, counting for a minute. "Everything's a little slow, but she looks sedated, so that's not a surprise. Her heart sounds healthy enough, but her breathing is a little more labored than I'd like to see."

"You noticed it too," the Doctor sighed. He pulled up a set of readings on the screen near the bed. "I took these with the sonic. What do you notice?"

"More brainwave activity than there should be," Rory said almost immediately. He'd been getting lessons in reading medical stats from the sonic, just in case there was ever a day when the Doctor couldn't help him with them. "She's sedated, but the brain is almost in a completely awake pattern."

"Which leads us to question if the sedation is wearing off, or if something happened to her to cause this," the Doctor said. He turned and looked at Lisa. "This is not going to be a pleasant night, Rory."


	7. Chapter 7

"So, Rory, what we have to ask ourselves is this; what happened to Lisa," the Doctor said, starting to pace back and forth. "You've heard me talk about the Cybermen, but you haven't had an encounter with them. Be thankful for that, Rory. They are nearly impossible to defeat. The Daleks aren't much better, but they wouldn't be this subtle with one of their victims. No, I think I can rule the Daleks out completely. They were interested in destroying the humans that day, not trying to create more Daleks. Not after they opened their jail at any rate. The Cybermen weren't expecting anyone other than humans at Canary Wharf, they thought it would be an easy infiltration point, somewhere they could work quietly until they were ready to establish themselves. Turn Canary Wharf into a conversion center. Oh, Rory, I'm missing something. I'm going to have to risk it. I don't want to, but I'm going to have to get Jack and Ianto in here and just hope that the universe doesn't implode."

"Doctor," Rory said, "what are you talking about?"

"Hush Rory, thinking," the Doctor said. "Sexy, will you call Jack and ask him to join us, please? Now don't take that tone with me, I know how dangerous this is, but I can't work this out on my own. We might have to hop back and take a look at Canary Wharf before the invasion began, see if they kept me away from something that I need to know. Put out the call, dear, and be nice to him. Jack loves you, you know. He's special."  
****  
Ianto was cleaning part of the coffee machine with a rag with Jack leaning against a railing watching him. "So you're telling me that what I learned about time at school is wrong," he said. "It's not a line, time travel is a real thing, events can be changed to re-write all of history and it's all a huge mess."

"Pretty much," Jack grinned. "Look at it this way, back in 1941 there was a site where a bomb was supposed to blow up. I landed a piece of space junk there trying to run a con on the Doctor and his companion at the time, Rose. Things went wrong, the Doctor managed to fix everything, I stole the bomb, and the Doctor rigged the space junk to blow up there instead. There was still an explosion, it got written off as a bomb site, but it wasn't. The bomb destroyed my ship in deep space just after the Doctor saved me from going with it."

"I'm glad he did," Ianto said. "Jack, what's that beeping noise?"

"Huh, I didn't know it could do that," Jack said. He flipped the cover shut on his vortex manipulator. "The TARDIS says that the Doctor wants to see us in the med bay. Looks like he's decided to bend the timelines even more. This must be more serious than I thought it was."

"I thought we couldn't go in there or the universe would explode."

Jack took Ianto's hand and started back towards where the TARDIS was parked. "The Doctor is a Time Lord, like I said. That means he knows more about time than anyone else," he said. "If he's asking us to join him even after he's said he's worried about timelines, that means there's more at risk than the universe." Jack reached out and touched the door. "Hey there, old girl, you know what's going on?"

"Jack?"

"She's alive, Ianto. Say hello."

"Uhm, hello."

Jack grinned and pushed the door open, stepping inside. "Whoa, okay, not going to ask about this," he said. "You're going to have to give me a hint on which way to go, old girl. I like what you've done with yourself, but I don't remember stairs."

"Hey," a man said from the top of the stairs, "you're Jack and Ianto, right? I'm Rory, one of the Doctor's friends. He wanted me to come get you so you didn't get lost and end up at the pool or something."

"Pool?" Jack said. "Oh man, he was holding out on me. I'm so going to give him a hard time about this. Lead the way, Rory. How long have you been traveling with the Doctor?"

"It's hard to say," Rory replied with a small smile. "My wife is the one who started traveling with him and I just tagged along until I realized it was where I wanted to be. The Doctor did say that we can't talk about much, something about the universe blowing up again. I've already been there, don't want to do it again."

"I don't blame you a bit," Jack said. "Hey Doctor, what happened?"

"Ah, Jack, good. Ianto too, brilliant," the Doctor said. "Rory is a good helper, but I need someone who knows the aliens I'm talking about, someone who was there that day. Someone who might know what Torchwood was hiding from me."

Ianto sat down in one of the chairs and looked over at Lisa. "I was only a junior researcher, Doctor," he said. "I was never allowed near any of the big projects, nothing that would tell me the inner workings of Torchwood. Lisa might know something, she was a higher rank than I was."

"Yes, well, we don't want to risk waking her up just now," the Doctor said. "There's far too much brainwave activity for me to feel confident that she's alone in there. Jack, you visited Torchwood One, what did you see?"

"Not nearly as much as I wanted to," Jack said. "They didn't trust me. I was always under an armed guard when I was there."

The Doctor looked over at him. "I know you, Jack, and I know how you operate."

"I didn't seduce my guards," Jack protested. The Doctor looked at him and raised an eyebrow. "Doctor, give me some credit."

"I am, it's how I know you saw more than they wanted you to," the Doctor said. "Jack, this is important. From what I remember of Canary Wharf, the ghost shifts had been going on for months. People were used to them. They'd grown comfortable believing the ghosts were just that. Torchwood didn't know what they were and they captured me before I could fully work it out. I think the Cybermen wanted the building at Canary Wharf, they wanted the people inside it, yes, but they wanted to appear slowly and silently, and I foiled that plan. No one was counting on the Daleks being there, least of all the Cybermen. No, I think this was an attempt to infiltrate the Earth and set up their first conversion center before anyone knew what was happening. It got out of control, as these things so often do, and they were defeated."

"There was a sub-basement," Ianto said. "No one but the top officials were allowed down there. I don't think it was even marked out on any plans for the building."

"How did you find out about it?" Jack asked, sitting down next to Ianto.

"I stumbled across a door when I was looking for a storage closet," Ianto said. "It was secured beyond anything else in the building so I left it alone, but I did ask my direct supervisor about it. He said that no one knew what was in there, but only the top bosses were allowed down there."

"Which means Jack should have been," the Doctor said. "I think, Jack, that I'm going to take a hop back and see exactly what they were keeping in that sub-basement. I'm wondering if it's something the Cybermen wanted, or if it was something completely unrelated to the whole battle."

"What about us?" Ianto asked. "Lisa?"

"You're here, you're part of the timeline now," the Doctor said. "Rory, you can go meet up with Pond if you want to."

"Nope, Lisa needs medical attention and I'm the best you've got," Rory said. "I'm staying."

"All right then, off we go," the Doctor said with a grin.


	8. Chapter 8

"Ianto Jones, what I need from you is a date after you found the sub-basement door before the battle day where you and Lisa would have been away from work," the Doctor said as he worked the console. "One day will do, a weekend would be better, but it'll be safer to the timeline if you both are out of the building in your time."

"Uhm, there was a weekend we took to go see her family," Ianto said. "A month before the battle, we left Friday after work and came back Monday."

"Perfect," the Doctor said. "No tricks now, girl, we need to slip in and slip out before they know we're there." He flipped a final switch and sent them into the time vortex.

Jack leaned against the railing, the only one other than the Doctor not holding on as the TARDIS shook, and grinned. "Same as ever, I see," he said. "I've missed you, Doctor."

"I know, Jack," the Doctor said. "I know more than you think I know. Remember, for me, you've already met the last me and we've talked. I answered all your questions for you and then we had an adventure."

"Sounds like old times," Jack said. "Doctor, answer one question for me. How badly would it screw things up if you stayed to work on the rift when we're done with this?"

"Badly, I'm afraid," the Doctor said. "However, if you're serious about wanting me to take a look at the rift, then I can come back after everything with the previous me."

"I'd like that," Jack said.

The Doctor looked at Rory and Ianto. "Jack, come with me for a minute, please," he said. "You two, don't touch anything. We've landed, but I need to check on a couple of things before we leave."

"What's going on, Doctor?" Jack asked, following the Time Lord up the stairs and into a room just off to the right.

"Jack, I know how you felt about me, how you may possibly still feel about me, but you have your young man out there," the Doctor said. "Ianto feels something for you, something deep if I'm any judge and, well, let's just say you may not like me when I come back."

"Why?"

"Spoilers, I'm afraid," the Doctor said. "Jack, you are one of the most special people I've had the honor of meeting and I would love to be able to have more with you, but you have your Ianto, and I'm, well, not available at the moment."

Jack nodded. "Do you think it's possible we'll be able to fix Lisa for Ianto?" he asked.

"I don't know," the Doctor said. "I don't believe so, but I've been proven wrong in the past. I don't want to get his hopes up though, so no mention of this to him just yet. Now, I've landed us in the sub-basement, Jack. What do you think they could have down here?"

"Whatever it is, Doctor, they've never put mention of it in paperwork or on the computer network," Jack said. "Hell, I knew about the sphere that ended up being a dalek prison, they had entered information about that into the network, but there's never been any mention of anything down here."

"So we're up against a complete unknown," the Doctor said. "Jack, I want to leave Rory and Ianto here for now. What do you think?"

"Ianto might try and wake Lisa up," Jack said.

"And Rory might help him." The Doctor sighed and rubbed his head. "All right, bad idea leaving them behind, but going into unknown danger is even worse."

"I'll keep them safe," Jack said. "I know I can never stay dead, Doctor. It's one thing I'm planning to ask you about, you know."

The Doctor looked sad for a moment. "Yes Jack, I remember it," he said. "All right, let's go see what's out there that's so secret Torchwood doesn't even trust itself to talk about it."  
***

The Doctor put Rory and Ianto in charge of flashlight. He wanted to have his hands free for his sonic screwdriver, and Jack wanted his hands free for his gun and other weapons. They moved slowly out into the hallway from the closet the TARDIS landed in, and looked around. "Tell me, Ianto, how does this compare to the rest of Torchwood One?" the Doctor asked, looking around.

"It's darker than the rest, not as well cared for, and smells damp," Ianto said, looking around. "It's hard to believe this is the same place I used to work."

"Yet it is," the Doctor said, studying the readout on the sonic. "Okay, so we need to ask the question, what is down here that's so special?"

"Doctor, I see locked doors," Jack said.

"Prisoners," the Doctor said, his tone dropping down. "Or test subjects. Either way, this part of Torchwood ends now."

Jack moved up and carefully shifted Ianto and Rory behind him. He recognized the tone in the Doctor's voice. "You guys wait here, keep watch for us," he said. "Rory, we might need your help in a minute, but stay here for now."

"Doctor?" Rory asked.

"Yes, Rory, stay put," the Doctor said absently. He was reading the clipboard that had been hanging next to the first locked door. "They have Silurians here, Jack. Six of them. Along with a Draconian, how did they get a Draconian on Earth, and several other alien species they aren't able to identify, but kept for research anyway."

"We need to get them out," Jack said.

"Of course we do, but this isn't what the Cybermen were looking for," the Doctor said. He was already working on the lock to the first door. "This isn't right, Jack. We're still missing something. There we go. Well, hello there. Jack, this is a baby Draconian. A baby, Jack."

"Breathe, Doctor," Jack said, putting his hand on the Doctor's shoulder.

"You're right." The Doctor picked up the baby and looked back towards the others. "Ianto, would you be able to hold her for me? She doesn't bite. My guess is she's only just hatched and is probably very hungry. We'll feed her when we get back to the TARDIS."

"Whatever you need, Doctor," Ianto said. He took the tiny form from the Doctor and held her against his chest. "I had no idea these were down here."

"I think almost no one did," the Doctor said. "Rory, you've dealt with the Silurians before, oh, but you won't remember it. Bother, timelines again. Go back to the TARDIS and get the secondary medbay ready for me, please. I don't want any of these poor hostages near Lisa until we work out what's going on here." He opened the second door and ducked. "Now that isn't very nice. I'm the Doctor and I'm here to help you, but you have to trust us. What clan are you from?"

"I won't answer your questions," the Silurian said.

"You're just making this harder on yourself," the Doctor sighed. "Can you walk? No, okay then, you'll have to be carried. If you hurt Jack, you'll be sorry you were ever rescued, do you understand? How many of your clan are here with you?"

"Five."

"One clan, could be much worse," the Doctor said. "You must have been found during construction, like my friend Madam Vastra was. Oh dear, so many problems. Jack, let's get the rest of these doors open and then we'll see what else they're hiding down here."

Jack nodded and picked up the Silurian. "You flinched when he mentioned Vastra. Do you know her?"

"I did. We grew up together. She didn't trust anyone, but if she befriended you, then I will trust you as well. Let me speak with my clan."

"Easy enough, then we're going to get you to safety," Jack said. "How many of your clan can walk?"

"Three. They will help carry the others."

"Doctor?"

"I heard Jack, thank you. Just bring him along here. There we go. Jack, you coordinate this, I'm going to see what else they have down here," the Doctor said. "Take them along to the TARDIS. Rory will show you where you need to go, then come back and find me. We'll get them taken care of."


	9. Chapter 9

Jack didn't want to leave Rory and Ianto alone with so many aliens, but when they got them into the medical bay and he was able to get a closer look at them, he realized that none of the people they'd just rescued would be able to fight. "We're going to need to feed everyone, old girl," Jack said, talking to the TARDIS. "Can you work out what would be best for everyone, something light that won't make them sick, while Rory checks them over?"

"Uhm, I actually have no idea how to check them over," Rory admitted.

"I do," Jack said. "Ianto, let me have that little one and you go with Rory to find the Doctor. I'll take care of our guests and get them fed. Tell the Doctor what's happened, will you? He wanted me with him."

Ianto nodded. "You'll be okay?"

"Yeah, I'll be fine. You guys be careful out there. Watch out for Torchwood employees. I don't want you getting caught by anyone," Jack said. "Tell the Doctor I'll be along as soon as I can."

Rory looked over at Ianto and shrugged. "Works for me, I guess," he said. "Come on, we need to figure out where the Doctor's wandered off to this time."

"Just look for the place where the most trouble can happen," Jack grinned. "That's where he'll be, right in the middle of it."

"True," Rory agreed.  
***

The Doctor left the prison cells behind him and kept going down the corridor, muttering to himself the whole time. Talking to himself was a habit he'd never broken, and one a lot of people never understood. "With the rift it's possible that anything from the whole of time and space could be down here, so the question I really need an answer to is what would Torchwood care enough about to hide away and not let anyone see? It's obvious they were holding people against their will for testing. Just because they aren't human doesn't mean they don't have feelings. Too bad I can't tell the leaders of Torchwood that, but I'm already causing enough ripples in this timeline, I don't need to mess it up any worse than I already have. So, okay, we have to assume that it's big and important whatever it is, and it's something that Jack would likely be able to recognize given that they keep him away from this part of the building all the time. Then again, they might have not wanted him to see the prisoners and that's why he was never allowed down here. Then again, it's possible they don't trust him even after all this time and they didn't want to let on there was more to Torchwood than he already knew. The original charter would still be in play here, even if the agreements with UNIT would have made it that much harder to try and take me captive."

"Doctor, who are you talking to?" Rory asked, catching up.

"Rory, what are you and Ianto doing here? I asked Jack to come with me."

"Yeah, well, we sort of had to switch jobs," Rory said. "I have no clue how to go about doctoring alien species and didn't want to hurt them worse. Jack said he knew how to patch them up so he sent us to meet up with you and he'll join us once everyone is settled and has food."

"I see, good old Jack," the Doctor said. "All right then, we're looking for something possibly big. Definitely alien, and not pleasant given that it's hidden so well and the Cybermen would want it."

"Something like that?" Ianto asked, pointing down a side corridor.

The Doctor stopped and turned around, looking where Ianto was pointing. "Oh, blimey, that's not good," he said. "You two stay here. Do not follow me for any reason, do you understand. That machine, if it's what I think it is, eats humans and I do not want to have to explain that to Jack or Pond. Understand?"

"Yes Doctor," Rory sighed. "We'll wait here for Jack."

"Oh bother. Jack. Do not let him near this. He would be a feast," the Doctor said. "Keep him here. Tell him that if he comes towards me I will leave him fully dressed, untied and in the control room with canisters of whipped cream and chocolate sauce left unused."

"How is that a punishment?" Ianto asked.

"You don't know Jack as well as I do," the Doctor replied. "I'll be right back, I just need to get some readings and then we are going to blow this machine up."

Ianto looked at Rory. "Does anything around the Doctor ever make sense?" he asked.

"Not really," Rory replied. "You sort of get used to it after a while."

"Seems like an unusual sort of life," Ianto said. 

"It is, but it's fun, and you get a lot of exercise," Rory said. "I'm in better shape now than I've ever been.That's not a bad thing."

"No, it's really not," Ianto agreed. "I suppose if I'd wanted an ordinary life I would have gone into maths at school."


	10. Chapter 10

"Jack, where are you, I need you in the control room now," the Doctor called, slamming the door to the TARDIS behind him. 

"I was just coming to join you," Jack said, hopping down the stairs. "I got all of our guests settled. They're asleep and the Bareel is watching the baby for me. We going to take them home, or back to their own time?"

"Yes, we will, Jack, or rather I will as I don't want to risk the timelines more than I have to," the Doctor said. "Come take a look at this. I found, or rather Ianto found, what they're hiding down here. There's a reason you were never allowed in this part of the building, Jack, and it wasn't the prisoners. Look at these readings."

Jack looked over the information on the monitor. "They don't."

"Yes."

"They didn't."

"They did."

"How?"

"I don't know."

"Can we?"

"Yes."

Rory cleared his throat. "Uhm, excuse me," he said. "Confused human here who doesn't have any telepathic abilities. What's going on?"

"That machine, Rory, is from the planet Zyfon," the Doctor said, starting to pace a little as he talked. "They were a lovely people, the Zyfon, but they had this one king who was insane. More insane than usual, more insane than anything you've ever seen before and he decided that his people needed to be controlled. That free will was bad and they were talking about him behind his back. Well, of course they were, they were trying to figure out how insane he was and how to get him off the throne before he completely destroyed their people."

"The Zyfon king figured out a way to implant a chip in the spinal column of all his people without them knowing about it," Jack said. "On them if just meant that they would believe whatever he said, do whatever he wanted and that made him happy. Of course, it also meant the end of their race when he died because the chips were coded to him and, with no one to give them orders, his people just wasted away."

"Humans, once they're spaceborn, found the planet and the machine that made the chips," the Doctor continued. "The machine ate them. Biology completely different, of course, and the machines ate the humans like candy. A rare few, however, were able to survive the process and formed a small army. They tried to take over a neighboring planet, were defeated and that should have been the end of it. I visited the planet after that and destroyed all the machinery that was there. I made sure that they would never be able to work again, so tell me how one of those machines is sitting just down the hall from where we are parked."

Ianto and Rory looked at each other. "That's not good," Rory said.

"No, it isn't," the Doctor said. "It isn't good because this means that Torchwood has something they should never have been able to find. This machine is not something that would have fallen through the rift. I don't understand how it is here, but that's what happened to Lisa, Ianto. That's why she has such advanced brain wave activity. She, somehow, was exposed to this machine and that's what's destroying her mind."

"Is there any way you can save her?" Ianto asked, sitting down.

"No, not from this," the Doctor replied. "The best I can do is take her to a world where she would be welcome, let her find a new home and a new purpose in life."

"Then do that, please. Even if it means I'll never see her again, she'd be alive," Ianto said.

"All right," the Doctor said softly. "I can do that for you. But first we have to destroy this machine here. Jack, how likely is it that Torchwood is kidnapping the homeless of London and bringing them in here to experiment on?"

"If they needed bodies that wouldn't be missed, probably pretty good," Jack said. "I never saw any notations about it though."

The Doctor sighed. "So many problems. Old girl, would you carefully hack into the computers here and download everything for me, please? I'm going to go and plant a bomb on that machine and ensure that it is a pile of scrap metal before we leave," he said. "Then we're going to take our rescued prisoners home and end this once and for all."  
***

The underground explosion that rocked part of London was written off as a gas line of some sort and was covered up by Torchwood. The Doctor took Jack and Ianto home first to protect what was left of the timeline. "Jack, a moment. I promise I won't keep him, Ianto."

"I'll be right there, Ianto," Jack said with a smile. "What's up?"

"Jack, I know what you're planning and what you want to do, but you have a young man there who just lost everything," the Doctor said. "Promise me one thing. As you're working with Ianto, let him know that if you ever have to leave suddenly, leave without explanation that you'll come back to him. Right now, you're all he has and he needs to know he's not going to lose that."

"I never went traveling with you again, did I, Doctor?" Jack asked.

"Spoilers again, Jack," the Doctor replied. "You'll see the old me in a few months, I'm not sure how many, it might be as long as a year, but it's close to time for that, Jack. Once I'm sure you're home, and the timelines aren't in danger, I'll pop back and look at the rift for you."

Jack pulled the Doctor into a hug. "What are you scared of?" he whispered.

"Oh, Jack, just remember one thing for me through everything," the Doctor said. "You are special, unique, and I couldn't survive without knowing you're there. Can you remember that for me?"

"I'll do my best," Jack said. "You don't know if I end up dating Ianto, do you?"

"I don't, it's not something you told me," the Doctor said. "Go on now, he needs you. I'll take our friends home, check to make sure there's no more nasty surprises at Torchwood one prior to the invasion, and then I'll be back." He pulled away and looked at Jack with sad eyes. "I promise I'll come back."

"I'll hold you to it," Jack grinned. "See you soon, Doc."

"Yes, Jack. Soon."


	11. Chapter 11

"What has you looking so sad?" Ianto asked the next morning when he brought Jack a mug of coffee.

"Just something the Doctor said to me last night," Jack replied. "Ianto, sit down a second. Look, I'm sorry about Lisa. I really thought the Doctor would be able to help and I got your hopes up."

"He did help, he was able to take her to a place where she'll be happy and alive," Ianto said. "That's a different fate than if she had remained here. I was going to break up with her, Jack, remember? I don't know what I'm feeling for you, but I want to find out. Is that something you still want?"

Jack grinned. "Oh yeah," he said. "Ianto, the Doctor also asked me something weird. He said to tell you, to make sure you know, that if I leave, I'm coming back."

"Are you planning on leaving, Sir?"

"No, but you know that I still need to find the Doctor, my Doctor, in the right timeline and ask him some questions," Jack said. "I want to know what happened to me, Ianto. He's the only one who can tell me, and you saw how careful he was about that when we were at Torchwood and in the TARDIS. I think it means there's something big coming. A fixed point in time that he can't change, can't tell me about, and I have to live through it."

"So does that mean we'll be continuing our lessons on time then, Sir?"

"Ianto, you keep calling me 'sir' in that tone and I'm going to strip you down here in my office," Jack said.

"I'll keep that in mind, Sir," Ianto smiled. "I should make coffee for the others so it will be ready when they arrive. Would you like to have dinner tonight, Jack?"

"Yeah, I'd like that, Ianto," Jack said. "Let's see where this goes."  
***

"Doctor, you didn't tell Jack everything, did you?" Rory asked once they'd dropped off the last of their rescued prisoners.

"No, I didn't," the Doctor replied. "Because I hurt him so badly in his future, Rory. So very badly, I'm surprised he doesn't hate me more than he already does. I made so many mistakes with him, so very many. I don't know why he called to ask me for help. Humans are so mysterious, you know."

Rory sighed. "What about Lisa? Will she really be okay?"

"She'll be fine. The commander of the base we left her at is an old friend and he'll keep an eye on her," the Doctor said. "I don't know how long of a life she'll have out here. There are many wars being fought, it's one reason they need soldiers, but with her mindset now, it's the only place I could leave her safely. Yes, she would have killed anyone around her if we'd left her somewhere else, and I'm not releasing a serial killer onto the universe. Now, let's go fetch Pond and see what's left of the subbasement of Torchwood, shall we?"

"I don't understand how all of this can just tie up so neatly," Rory sighed.

"It hasn't, yet," the Doctor said. "There's still a few pieces that need to be looked after, but I can do all of that from here. Remember, I have a way into the Torchwood computers now. That's actually cool. I've never had that before."

"I don't understand exactly what Torchwood even is," Rory said.

"I suppose you could say that Torchwood is my fault," the Doctor said. He leaned against the railing and ran a hand over his face. "I helped the Queen battle a werewolf that turned out to be an alien that had been living on Earth for hundreds of years. She formed Torchwood after I'd left to defend the planet against aliens. Against me. I had a hard time believing that Jack went to work for them, back when I found out, but then I realized he really didn't have a choice. What else would he do?"

"Are we really going back to help him?"

The TARDIS landed. "I am," the Doctor said. "You and Pond will just have to go and live your lives for a while and I'll pick you up again when I'm finished. I don't want the pair of you around the rift unless you absolutely have to be."

"So does that mean we're not telling Amy about what we've been doing?" Rory asked.

"I'd rather not. My arm still hurts from the last time she punched me," the Doctor replied. "Go and see if you can find her. I'll wait here."  
***

When Jack stood at the end of the universe and faced the Doctor, he realized two things. He hated the one he saw in front of him, so cold and so dismissive. He also realized he could still hear his Doctor's words and held onto them tightly as the Doctor in front of him tried to destroy him.

**Author's Note:**

> http://www.amazon.com/The-Nightmare-ebook/dp/B00AZLLEMW/ref=sr_1_1?ie=UTF8&qid=1357862075&sr=8-1&keywords=Lexxie+Scott
> 
>  
> 
> I just published my first original novella. If you like my fan fiction, please take a look. :-)


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